Sequence dependence of the helical repeat of DNA in solution

Peck, Lawrence J.; Wang, James C.

doi:10.1038/292375a0

Cited by 317 publications

(162 citation statements)

References 21 publications

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“…It is known, for example, that dðAÞ n · dðTÞ n polynucleotide has a helical structure that is different from canonical B form (30)(31)(32). If such is the case, one has to use fragments with longer repeating sequence motifs for the elemental set.…”

Section: Resultsmentioning

confidence: 99%

Sequence dependence of DNA bending rigidity

Geggier

Vologodskii

2010

Proc. Natl. Acad. Sci. U.S.A.

212

247

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For many aspects of DNA-protein interaction, it is vital to know how DNA bending rigidity (or persistence length, a) depends on its sequence. We addressed this problem using the method based on cyclization of short DNA fragments, which allows very accurate determination of a. Our approach was based on assigning specific values of a to each of 10 distinct dinucleotide steps. We prepared DNA fragments, each about 200 bp in length, with various quasiperiodic sequences, measured their cyclization efficiencies (j factors), and fitted the data by the theoretical equation to obtain the values of a for each fragment. From these data, we obtained a set of a for the dinucleotide steps. To test this set, we used it to design DNA sequences that should correspond to very low and very high values of a, prepared the corresponding fragments, and determined their values of a experimentally. The measured and calculated values of a were very close to one another, confirming that we have found the correct solution to this long-standing problem. The same experimental data also allowed us to determine the sequence dependence of DNA helical repeat.DNA elasticity | DNA persistence length T he value of DNA persistence length, a, closely related to the bending rigidity of the double helix, is very important for quantitative analysis of many aspects of DNA functioning. Many different methods were applied over the last decades to determine this value and its dependence on ionic conditions (1). These studies showed that under near physiological ionic conditions the value of a is close to 50 nm (1-3). They also showed that, in a good approximation, the value of a does not depend on DNA sequence, because many studies that use different DNA molecules gave very close values of a. However, the sequence dependence of DNA bending rigidity is vital for many aspects of DNAprotein interaction, and is particularly important for understanding how nucleosomes position along DNA molecules (4, 5). Despite its importance, the problem has formerly remained unsolved, although a few research groups have tried various approaches (6-8). The data that are generally considered most reliable were obtained from statistical analysis of DNA-protein crystal structures (9, 10). The large volume of available structural data allowed this group of researchers to present a very detailed picture of the sequence dependence of DNA conformational properties. This analysis, however, is based on the assumption that variations of the DNA bend angles in the crystals correspond to the amplitudes of thermal fluctuations of these angles in solution. It is hard to justify this assumption.The major obstacle in determining the sequence dependence of a is the necessity of highly accurate measurements of a for different sequences. The majority of methods applied for the measurements of a do not provide the necessary level of accuracy. The only known method that allows one to measure a with the required accuracy is based on cyclization of short DNA fragments by DNA ligase (2,3,11,12). It i...

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Section: Resultsmentioning

confidence: 99%

Sequence dependence of DNA bending rigidity

Geggier

Vologodskii

2010

Proc. Natl. Acad. Sci. U.S.A.

212

247

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“…where g is the DNA helical repeat, equal to 3.55 nm (Peck & Wang, 1981). The value of C is set to 2 Â 10 À19 erg cm (Hagerman, 1988).…”

Section: Dna Modelmentioning

confidence: 99%

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition

Jian

Schlick

Vologodskii

1998

Journal of Molecular Biology

104

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“…The single crystal x-ray analyses of both B-DNA (1-3) and A-DNA (4)(5)(6)(7) have revealed large variations in the helix parameters. Furthermore, the twist angle of the helix has been shown to depend on sequence when the molecule is in solution, both by the effects on supercoiling parameters when short segments of known sequence are inserted into closed circular DNA (8)(9)(10) and by the nuclease digestion patterns of DNA adsorbed on surfaces (11,12). These variations in helix geometry may play an important role in the recognition of specific sequences by proteins.…”

Section: Introductionmentioning

confidence: 99%

A molecular mechanical model to predict the helix twist angles of B-DNA

Tung

Harvey

1984

Nucl Acids Res

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We present here a model for the prediction of helix twist angles in B-DNA, a model composed of a collection of torsional springs. Statistically averaged conformational energy calculations show that, for a specified basepair step, the basepair-basepair conformational energy is quadratically dependent on the helix twist angle, so the calculations provide the spring parameters for the basepair-basepair interactions. Torsional springs can also be used to model the effects of the backbone on the helix twist, and the parameters for those springs are derived by fitting the model to experimental data. The model predicts a macroscopic torsional stiffness and a longitudinal compressibility (Young's modulus) which are both in good agreement with experiment. One biological consequence of the model is examined, the sequence specificity of the Eco RI restriction endonuclease, and it is shown that the discriminatory power of the enzyme receives a substantial contribution from the energetic cost of torsional deformations of the DNA when wrong sequences are forced into the enzyme binding site.

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Sequence dependence of the helical repeat of DNA in solution

Cited by 317 publications

References 21 publications

Sequence dependence of DNA bending rigidity

Sequence dependence of DNA bending rigidity

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition

A molecular mechanical model to predict the helix twist angles of B-DNA

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